Research Activities:
Matthew Wakefield specializes in the application of high throughput sequencing and microarray technologies to the understanding of the control and stability of gene expression.
Current projects include:
- Systems biology of chemotherapeutic drug resistance in a mouse cancer model
- Improved analysis techniques for RNAseq
- Design of RNAseq experiments including estimation of power
- Epigenetic stability in cancer and aging
- Comparative genomics approaches to identifying epigenetic regulatory control elements
He was an author on the proposal to sequence the genome of a model Australian marsupial (Macropus eugenii - the tammar wallaby) and continues to work in collaboration with the ARC Centre for Kangaroo Genomics and the Kangaroo Genome Project.
He is the primary author of the Vestige maximum likelihood phylogenetic footprinting package that is built using the PyCogent toolkit and a contributor to the PyCogent package.
Selected Publications
Oshlack A & Wakefield MJ (2009) 
Transcript length bias in RNA-seq data confounds systems biology
Biology Direct 4:14
doi:10.1186/1745-6150-4-14
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Warren WC, Hillier LW, Graves JAM, Birney E, Ponting CP, Grutzner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang S, Heger A, Locke D, Miethke P, Waters PD, Veyrunes F, Fulton L, Graves T, Puente XS, Lopez-Otin C, Ordonez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Aslop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Renfree M, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell N, Buschiazzo E, Jentzsch IV, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison E, Sachidanandam R, Smith C, Stark A, Kheradpour P, Hannon G, Rens W, Ferguson-Smith M, Lefevre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhard R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux J, Niwa H, Sekita Y, Flicek P, Webber C, Hardison R, Washington University Genome Sequencing Center,
Mardis ER & Wilson RK. (2008)
Genome analysis of the platypus reveals unique signatures of evolution
Nature 453(7192):175-183
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New York Times
ABC News
BBC World
The Age
Nobel Intent
New Scientist
ABC Science
Video:
ABC News
ABC News (Extended)
Audio:
ABC Radio 'AM'
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Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SMJ, Sharpe T, Baker M, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD, Oda M, Papenfuss AT, Parra ZE, Pollock DD, Ray DA, Schein JE, Speed TP, Thompson K, VandeBerg JL, Wade CM, Walker JA, Waters PD, Webber C, Weidman JR, Xie X, Zody MC, Broad Institute Genome Sequencing Platform, Broad Institute Whole Genome Assembly Team, Graves JAM, Ponting CP, Breen M, Samollow PB, Lander ES, Lindblad-Toh K (2007)
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
Nature 447:167-177.
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ABC Online, ABC Science, BBC News, Nobel Intent, The Australian (10th May Page 8), The Sydney Morning Herald (10th May Page 12), COSMOS, New Scientist, ABC Regional - AM,
The Science Show
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Gentles AJ, Wakefield MJ, Kohany O, Gu W, Batzer MA, Pollock DD, and Jurka J (2007)
Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica
Genome Research 17:992-1004.
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Knight R, Maxwell P, Birmingham A, Carnes J, Caporaso JG,
Easton BC, Hamady M, Liu Z, Lozupone C, Sammut R,
Smit S, Wakefield MJ, Widmann J, Wikman S, Wilson S,
and Huttley GA (2007)
PyCogent: a toolkit for making sense from sequence
Genome Biology 8:R171
Online Resources: PyCogent SourceForge Repository
Publication List
ISI Researcher ID A-7795-2008
Software
GnuPG / OpenPGP Key
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